You can make a transparency map , and try to hide them . Or you can use magnets , and attempt to deform them flat. Deforming them is going to leave an ugly surface .    You can use the group editor , and make a new group for those bits , and then make that group transparent . Group editor may actually be the easiest way , work in front or side view wireframe and one select with the selection box should get it .

The best solution is to bring them into  a modelling program and clean up the model.

? why do you need them flat ?   you can just poke the bottom edge through the ground as long as its not going to be seen.